You could check the correctness of the exported data by loading it back into the OS/2 system (of course into a different table).
If that works, a possible problem could be (just guessing) a difference in codepages, with a certain character from the source codepage missing in the target codepage.
If that's the case, try loading into a UNICODE-encoded table.
An other problem could be the "physical" transfer of the data file between the two systems: did you make sure to copy it (with FTP or whatever) in BINARY mode?
Or did you ZIP it? In that case, using GNU zip instead of winzip could solve the problem...